This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Next-generation sequencing (NGS) studies have led to dramatic improvements in our understanding of human microbiomes. However, this method is based on the presence of DNA and cannot distinguish between living and dead microbes on its own. Environments like our skin are hostile and have high microbe turnover, which leads to significant amounts of DNA from dead microbes, which can lead to inaccurate community estimations in NGS studies. To overcome this, researchers tested the feasibility of pre-treatment with Benzonase to digest unprotected DNA. They used both mock bacterial communities and skin microbiome samples with inactivated bacteria or bacteria-free DNA spiked-in. Benzonase (BDA) pre-treatment reduced the levels of DNA from dead bacteria in both mock and natural communities. It also reduced the amount of host DNA in samples with high human-to-microbial DNA ratios without obvious impact on the microbial profile..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Metagenomic analysis frequently plays an important role in development pipelines for human fecal microbiome-related products, but validation and standardization of the methods used to extract DNA and assemble sequence libraries for these studies is currently lacking. To close this gap, researchers recently characterized existing protocols for accuracy and precision. First, they tested the quantification accuracy by using a defined mock community of bacteria. Then, the protocols that performed as expected were evaluated for both within- and inter-laboratory precision metrics. The protocols were also tested against the MOSAIC Standards Challenge samples. Lastly, they defined performance metrics for the recommended protocols to provide best-practice guidance. The uptake of the recommendations generated here should improve reproducibility in human metagenomic research and therefore facilitate development and commercialization of human microbiome-related products..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

CREATES is a set of 6 steps that help learners read and critically analyze scientific papers. The CREATES method, pioneered by Dr. Sally Hoskins, has a demonstrated positive impact on undergraduate students' self-confidence in scientific reading, as well as in their general perceptions of and beliefs about science and scientific thinking (Hoskins, et. al, 2017).

The new CREATES site, created in collaboration with Jordan Moberg Parker, UCLA's Director of Undergraduate Laboratory Curriculum and Assessment in Microbiology, Immunology, and Molecular Genetics, uses interactive media, step-by-step directions, and detailed annotation of authentic examples to guide students through the process.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"The development of long-read sequencing has allowed for the generation of more complete and contiguous genomes in metagenomics studies. However, long-reads are more prone to sequencing errors than short-reads, and these errors can end up incorporated in the draft genomes. Combining short- and long-reads can overcome such errors, but is computationally taxing. To avoid this, researchers developed the ‘Hierarchical Clustering Based Hybrid Assembly (HCBHA) approach.’ This approach first groups the long- and short-reads into candidate bacterial haplotypes and then assembles each group separately, which reduces the computational demand . Researchers tested this framework on a microbiome from activated sludge, an important part of wastewater treatment. The highly complex microbiomes found in activated sludge remove pollutants from wastewater..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"High-quality reference genomes are needed to understand the physiology and function of uncultured microbes in complex ecosystems. Metagenomics has been an incredibly useful tool for studying microbial communities, but assigning sequence assemblies accurately to genomes is difficult in microbial species or strains that lack a reference genome. These 'consensus genomes' have lower resolution than those generated from cultured isolates. Combining single-cell genomics with metagenomics may allow us to overcome these methodological weaknesses. Thus, researchers recently developed a framework called SMAGLinker, which integrates single-cell genomes from microfluidic droplets and uses them as guides for metagenome assembly. Compared to metagenomics alone, SMAGLinker showed more precise contig binning and higher recovery rates of rRNA and plasmids in a mock microbial community. In human gut and skin microbiota samples, SMAGLinker returned more genomes than the conventional metagenomics frameworks..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This course will conduct a comparative study of the grand strategies of the great powers (Britain, France, Germany and Russia) competing for mastery of Europe from the late nineteenth to the mid-twentieth century. Grand strategy is the collection of political and military means and ends with which a state attempts to achieve security. We will examine strategic developments in the years preceding World Wars I and II, and how those developments played themselves out in these wars. The following questions will guide the inquiry: What is grand strategy and what are its critical aspects? What recurring factors have exerted the greatest influence on the strategies of the states selected for study? How may the quality of a grand strategy be judged? What consequences seem to follow from grand strategies of different types? A second theme of the course is methodological. We will pay close attention to how comparative historical case studies are conducted.

In our daily lives we use hundreds or even thousands of products and services. They are all designed, some with more success than others. The ‘Delft Design Approach’ is a structured approach that helps designers to tackle complex design challenges: from formulating a strategic vision, to mapping user behaviors, their needs and their environment, to developing and selecting meaningful proposals for products and services.

DDA691x offers a college-level introduction to the Delft Design Approach through lectures and exercises on design fundamentals and 6 methods. You will understand basic models and concepts that underlie the Delft approach. You will also develop the capability to use 6 basic methods in a design context. You will do so by applying the methods to realistic design challenges and by reflecting on your own performance by comparing it to that of expert designers as well as through peer discussion.

Engineering systems design must have the flexibility to take advantage of new opportunities while avoiding disasters. This subject develops “real options” analysis to create design flexibility and measure its value so that it can be incorporated into system optimization. It builds on essential concepts of system models, decision analysis, and financial concepts. Emphasis is placed on calculating value of real options with special attention given to efficient analysis and practical applications. The material is organized and presented to deal with the contextual reality of technological systems, that substantially distinguishes the analysis of real options in engineering systems from that of financial options.
Note
This MIT OpenCourseWare site is based on the materials from Professor de Neufville’s ESD.71 Web site. Additional materials, updated as needed by Professor de Neufville, can be found there.

This course is the scientific communications portion of course 7.02, Experimental Biology and Communication. Students develop their skills as writers of scientific research, skills that also contribute to the learning of the 7.02 course materials. Through in class and out of class writing exercises, students explore the genre of the research article and its components while developing an understanding of the materials covered in the 7.02 laboratory.

This course investigates theories and practices of feminist inquiry across a range of disciplines. Feminist research involves rethinking disciplinary assumptions and methodologies, developing new understandings of what counts as knowledge, seeking alternative ways of understanding the origins of problems/issues, formulating new ways of asking questions and redefining the relationship between subjects and objects of study.
What makes research distinctively feminist lies in the complex connections between epistemologies, methodologies and research methods. This course explores how these connections are formed in the traditional disciplines and raise questions about why they are inadequate and/or problematic for feminist inquiry and what, specifically, are the feminist critiques of these intersections.
This course is part of the Graduate Consortium in Women’s Studies at MIT.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Host-microbiome interactions are a critical component of host health, and plants have a particularly complex relationship with their microbiomes. Understanding these functional relationships will allow us to predict, and even influence, host fitness. Many ‘-omics’ techniques have been developed, and each is a powerful tool solo, but combining them opens the door to a more holistic, systems-level understanding. This strategy, called holo-omics, requires careful experimental design and faces several challenges as a field. First, it currently lacks well-tested analytical frameworks. Second, there is a need for freely available, specialized bioinformatics tools, as most focus on just one data source and don't integrate host and microbe data. Lastly, the heterogeneous nature of holo-omics data requires a wide range of expertise - including plant biologists, microbe experts, statisticians, and computational biologists..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Word Count: 6872

(Note: This resource's metadata has been created automatically by reformatting and/or combining the information that the author initially provided as part of a bulk import process.)

Observational physical oceanography includes topics such as the  physical description of the sea, the physical properties of seawater, methods and measurements, wind-driven ocean circulation, abyssal ocean circulation, boundary processes, and wave motions.

This course is an introduction to software engineering, using the Java™ programming language. It covers concepts useful to 6.005. Students will learn the fundamentals of Java. The focus is on developing high quality, working software that solves real problems.
The course is designed for students with some programming experience, but if you have none and are motivated you will do fine. Students who have taken 6.005 should not take this course. Each class is composed of one hour of lecture and one hour of assisted lab work.
This course is offered during the Independent Activities Period (IAP), which is a special 4-week term at MIT that runs from the first week of January until the end of the month.

This course is an introduction to software engineering, using the Java™ programming language. It covers concepts useful to 6.005. Students will learn the fundamentals of Java. The focus is on developing high quality, working software that solves real problems.
The course is designed for students with some programming experience, but if you have none and are motivated you will do fine. Students who have taken 6.005 should not take this course. Each class is composed of one hour of lecture and one hour of assisted lab work.
This course is offered during the Independent Activities Period (IAP), which is a special 4-week term at MIT that runs from the first week of January until the end of the month.

We now know how to analyze pure compounds, but what if we have a mixture? Spectrophometry becomes quite complex when dealing with multiple species of compounds at once. In order to purify a compound we can separate if from a mixture based on its intrinsic chemical properties. Remember that fluorescein is negatively charged at a pH above pKa of the carboxyl group. We can take advantage of this fact and use its attraction to positive charges to separate it from other molecules. In ion-exchange chromatography, we will use a stationary phase with a positive charge, allowing negatively charged molecules to bind and positively charged species to flow through. We can then disrupt this interaction and retrieve our now-purified molecule, and use spectrophotometric analysis of our purified fractions to determine how well we were able to separate our molecules.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Ruminants are the only animals not dependent on dietary amino acids as a source of nitrogen. They have ureolytic bacteria in their rumen that hydrolyze urea into ammonia and use it as a nitrogen source. However, very few ureolytic bacteria have been isolated and studied in pure culture to date. To close this gap, researchers established and used a new integrated approach on bacteria from cattle rumens. They started with urease gene (ureC) guided enrichment and then embedded single cells in agarose microspheres for in situ cultivation. This allowed them to isolate and characterize diverse ureolytic bacteria with demonstrated urease activity. The researchers sequenced a subset of the isolated bacteria and found 28 strains from 12 species with urease genes. These bacterial species had not previously been found in the rumen, but this team detected them in metagenomes from 6 ruminant species. The new strains contained unique genes compared to known related strains, indicating new metabolic functions..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This course focuses on introducing the language, libraries, tools and concepts of Javaᵀᴹ. The course is specifically targeted at students who intend to take 6.170 in the following term and feel they would struggle because they lack the necessary background. Topics include: Object-oriented programming, primitives, arrays, objects, inheritance, interfaces, polymorphism, hashing, data structures, collections, nested classes, floating point precision, defensive programming, and depth-first search algorithm.

Is there a difference in citation rates between articles that were published with links to data and articles that were not? Besides being interesting from a purely academic point of view, this question is also highly relevant for the process of furthering science. Data sharing not only helps the process of verification of claims, but also the discovery of new findings in archival data. However, linking to data still is a far cry away from being a "practice", especially where it comes to authors providing these links during the writing and submission process. You need to have both a willingness and a publication mechanism in order to create such a practice. Showing that articles with links to data get higher citation rates might increase the willingness of scientists to take the extra steps of linking data sources to their publications. In this presentation we will show this is indeed the case: articles with links to data result in higher citation rates than articles without such links. The ADS is funded by NASA Grant NNX09AB39G.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"NOTCH1 is a protein implicated in various diseases, including breast cancer. In order to control Notch signaling, researchers have developed a light-activated tool called OptoNotch. OptoNotch is an engineered form of NOTCH1 that is activated under blue light. This mimics NOTCH1’s natural activation program: activation, release from the plasma membrane, translocation to the nucleus, and initiation of potentially harmful expression of different genes. The ability to activate NOTCH1 using only light makes OptoNotch highly targeted and easier to implement than chemical- or genetic-based systems. When deployed in two lines of breast cancer cells, OptoNotch could track how NOTCH1 contributed to accelerated cell proliferation, as well as cell migration, the phenotype of cancer cells in 3D cultures, mimicking patients' tumors, and resistance to common chemotherapy drugs. OptoNotch could help scientists to understand the roles of NOTCH1 in normal and disease conditions, and help screen for promising drug candidates..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.